title: C28/I2 cells, siC9orf72_2

city: Hangzhou

first: Yutao

last: Zhu

address: East Qing Chun Road

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine,

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: C28/I2 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: siRNA was transfected using iMAX

value: chondrocyte cell line

value: C9orf72 knockdown

value: Day 3


title: C28/I2 cells, siC9orf72_3

status: Public on May 01 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Ctrl_3

city: Chengdu

first: Xin

last: Zheng

state: Sichuan

address: No. 14, Section 3, Renmin South Road

institute: Sichuan University

data_processing:
The raw paired-end reads were trimmed, and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the fragments per kilobase million (FPKM) method.
Differential expression genes (DEG) analysis was performed using the DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with FPKM for every gene and every sample.
Supplementary files format and content: only one processed data file

growth_protocol: Cells were routinely cultured in Dulbecco's modified Eagle medium (DMEM; Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (FBS) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA were extracted and purified using MiniBest Universal RNA Extraction kit (Takara, Japan) according to the manufacturer’s instruction.
The cDNA library was prepared following the procedures of TruSeqTM RNA sample preparation kit (Illumina, San Diego, CA) using 1μg total RNA

treatment_protocol: The cells cultured were grown to ~90% confluency, followed by treatemnt of 5 μg/mL FnEVs or PBS for 2 hr at 37°C in a humidified 5% CO2 atmosphere.

value: PBS


title: M787AAA_T2_scR_CEL-Seq2

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

description:
CelSeq-2
Pretreatment NBL M787AAA_T2

library_source: transcriptomic single cell

data_processing:
Failed reactions were identified by low levels of ERCC external RNA controls and excluded. Furthermore, a liveness threshold was calculated for each plate based on the wells with no cell added, in order to distinguish live cells from dead and/or apoptotic cells. This threshold was set to a minimum of 500 transcripts.
Assembly: hg38 Patch 10 human genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: NBL tumor left adrenal gland

extract_protocol:
Tumor material was collected in the operating room by Truecut biopsy (samples at diagnosis) or surgical resection (debulking procedure after induction chemotherapy). The Dutch samples were gently dissociated into single‐cells and sorted by flow cytometry for single‐cell RNA sequencing using the CEL‐Seq2 platform. In brief, preparation of the tumor pieces for single‐cell RNA sequencing was started within 4 hours after the surgery. The material was minced into pieces <1mm3 and dissolved by enzymatic digestion with collagenase I, II and IV (2.5 mg/mL) at 37°C with agitation for max. 1 hour. The samples were filtered through a 70 μm cell strainer and washed in DMEM. Cells were further separated into a single cell suspension with the NeuroCult dissociation kit according to the manufacturer's protocol (StemcellTM Technologies, cat#05707), washed and stained with DAPI and DRAQ5. Next to this unbiased strategy, some samples were additionally stained with antibodies to enrich for T cell populations (NB124, NB125 with CD3‐PE (Biolegend, cat#300308); NB124 with TCRγδ‐BV421 (Biolegend, cat#331217) or with GD2‐FITC (BD Biosciences, cat#563439) to enrich for tumor cells (000GGU, 000GXF, NB106, NB107, NB098, NB125, NB125, NB130, NB152). Single live cells were sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a FACSJazz, FACSAria II or Sony SH800S machine and subsequently spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing. Peripheral blood mononuclear cells (PBMC) from 5 healthy young adult donors (mean age 28) were isolated by Ficoll-Paque (VWR) density centrifugation and stained with fixable viability dye efluor506 (eBioscience, cat#65‐0866‐14), CD3‐PE (Biolegend, cat#300308) and CD56‐APC (Biolegend, cat#318310) antibodies. Subsequently, live CD3+ T cells and CD56+ NK cells were FACS sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a Sony SH800S machine. The plates were spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing.
All samples were processed for total transcriptome amplification, library preparation and sequencing into Illumina sequencing libraries as previously described70. Paired‐end 2x75 bp sequencing read length was used to sequence the prepared libraries using the Illumina NextSeq sequencer. Sharq preprocessing and QC pipeline were applied to process the single‐cell RNA‐seq data as described71. Read mapping was done using STAR version 2.6.1 (RRID:SCR_004463) on the hg38 Patch 10 human genome. Function featureCounts (RRID:SCR_012919) of the subread package (version 1.5.2) was used to assign reads based on GENCODE version 26 (RRID:SCR_014966).

tag: tissue

value: NBL tumor left adrenal gland

tag: tumor type

value: High-risk NBL

tag: tumor stage

value: pre-treatment

tag: Sex

value: female

value: CDK4 amplified


title: popliteal, males from infected mothers, rep1, ADT-derived cDNA

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

country: USA

institute: University of Utah

description:
INF_Male_SP
protein

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, V(D)J and ADT) was performed using the 10x Genomics Cell Ranger pipeline where ADT and V(D)J sequences were treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis) for mRNA and ADT. V(D)J was processed using scRepertoire.
Assembly: mm10-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: 10x Genomics output files.
Supplementary files format and content: filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Female_GEX_filtered_feature_bc_matrix-2.h5: mRNA/transcript of germinal center B cells.
Supplementary files format and content: INF_Female_SP_filtered_feature_bc_matrix.h5: Surface protein information.
Supplementary files format and content: INF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: INF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Female_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Library strategy: CITE-seq

molecule: polyA RNA

organism: Mus musculus

source_name: Popliteal lymph node

extract_protocol:
The popliteal lymph node of mice born from S. mansoni infected mothers or control mothers were harvested 14 days after footpad immunization with 1.10th the dose of a commercial Tetanus/Diphtheria vaccine. Lymph nodes were smashed through a 70um filter to form a single cell suspension and washed before pelleting and staining. Primary antibody staining was done for 30 minutes in the dark at 4 degrees and washed twice before cell sorting on a FACS Aria. After sorting, cells were stained with FITC-conjugated Tetanus Toxoid for 15 minutes and then the anti-FITC TotalSeq antibody per manufacturer's instruction. Cells were counted and resuspended at a concentration of 10,000 cells/ul before proceeding to library construction.
Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and amplified by PCR according to the Chromium Single Cell 5’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. For all cDNA library preparations, we further proceeded according to the manufacturer’s instructions for Single Cell 5’ v2 protocol (10x Genomics). mRNA and ADT sequences were combined in Cell Ranger, outputting one file per sample for those two libraries.
V(D)J library: Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics).
CITEseq library: Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics).

value: Popliteal lymph node

value: Germinal Center B cells

tag: condition

value: Born to S. mansoni infected mothers

value: Male

tag: antibodies/tags

value: TotalSeq-C0988 anti-FITC Antibody


title: Liver, tolerant/T, 1

city: Shanghai

first: Yuan

last: Liu

address: No. 160 Dongchuan Rd.

institute: Renji Hospital

data_processing:
Cutadapt 4.4 was used to find and removes adapter sequences and low quality sequences
Hisat2 was applied for sequence mapping
StringTie was used for the assembly of RNA-Seq alignments into potential transcripts and Ballgown was used for FPKM calculation
Assembly: GRCh37
Supplementary files format and content: Excel file containing FPKM values for each sample

source_name: Liver

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) and enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). 1-2ug of RNA was used for library construction.
RNA library for RNA sequecing was prepared by KAPA Stranded RNA-Seq Library Prep Kit(Illumina)

value: Liver


title: Ctrl_1


title: C28/I2 cells, siC9orf72_1


title: Ctrl_2


title: popliteal, males from infected mothers, rep1, mRNA-derived cDNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, V(D)J and ADT) was performed using the 10x Genomics Cell Ranger pipeline where ADT and V(D)J sequences were treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis) for mRNA and ADT. V(D)J was processed using scRepertoire.
Assembly: mm10-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: 10x Genomics output files.
Supplementary files format and content: filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Female_GEX_filtered_feature_bc_matrix-2.h5: mRNA/transcript of germinal center B cells.
Supplementary files format and content: INF_Female_SP_filtered_feature_bc_matrix.h5: Surface protein information.
Supplementary files format and content: INF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: INF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Female_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.


title: popliteal, females from infected mothers, rep1, V(D)J-derived cDNA

description:
INF_Female_VDJ
V(D)J/BCR

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, V(D)J and ADT) was performed using the 10x Genomics Cell Ranger pipeline where ADT and V(D)J sequences were treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis) for mRNA and ADT. V(D)J was processed using scRepertoire.
Assembly: mm10-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: 10x Genomics output files.
Supplementary files format and content: filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Female_GEX_filtered_feature_bc_matrix-2.h5: mRNA/transcript of germinal center B cells.
Supplementary files format and content: INF_Female_SP_filtered_feature_bc_matrix.h5: Surface protein information.
Supplementary files format and content: INF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: INF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Female_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Library strategy: V(D)J

value: Female


title: C28/I2 cells, siNC_3

value: WT


title: M609AAA_T1_scR_CEL-Seq2_2

description:
CelSeq-2
Pretreatment NBL M609AAA_T1

source_name: NBL tumor left cervical primary tumor

value: NBL tumor left cervical primary tumor

value: MYCN non-amplified


title: C28/I2 cells, siNC_2

value: chondrocyte cell line

value: Day 3


title: Cal29_siCT_1

city: Freiburg

first: Sainab

last: Totonji

address: Breisacherstraße 66

country: Germany

institute: Uniklinik Freiburg

description:
Cal29_siCT_1
Count_table_bladder_Cal29.txt

data_processing:
STAR
Trimmed sequence reads were mapped to hg19 using STAR (parameters --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate  --limitBAMsortRAM 60000000000)
Read count extraction and normalization were performed using homer(analyzeRepeats.pl and edgeR)
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: RNA was extracted from 5637 and CAL-29 BC cell lines at day 3 after siRNA treatment.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). f total RNA was used for the construction of sequencing libraries.
RNA librairy was constructed at Novogene following standard protocols

value: Bladder cells

value: siCT


title: U251shA2B1 3

city: xi'an

first: Liangliang

last: Shen

address: West changle road 169

institute: The fourth military medical university

data_processing:
2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Assembly: mm10
Supplementary files format and content: The data related to gene counts and FPKM values were listed in the folder "1_genes_fpkm_expression.txt "

source_name: cell line

extract_protocol:
RNA was harvested usingTRIzol reagent (Invitrogen, Carlsbad, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: cell line

value: Glioma

value: hnRNPA2B1 knockdown


title: M609AAA_T1_scR_CEL-Seq2_1

description:
CelSeq-2
Pretreatment NBL M609AAA_T1

value: High-risk NBL

value: pre-treatment

value: female


title: popliteal, females from infected mothers, rep1, mRNA-derived cDNA

value: Popliteal lymph node

value: Germinal Center B cells

value: Born to S. mansoni infected mothers


title: U251shA2B1 2


title: C28/I2 cells, siNC_1


title: popliteal, females from infected mothers, rep1, ADT-derived cDNA

description:
INF_Female_SP
protein

value: Female

value: TotalSeq-C0988 anti-FITC Antibody


title: M609AAA_T1_scR_CEL-Seq2

description:
CelSeq-2
Pretreatment NBL M609AAA_T1

value: NBL tumor left cervical primary tumor


title: M609AAA_T1_scR_CEL-Seq2_3

description:
CelSeq-2
Pretreatment NBL M609AAA_T1

value: MYCN non-amplified


title: M017AAB_T1_scR_CEL-Seq2_2

description:
CelSeq-2
Pretreatment NBL M017AAB_T1

value: NBL tumor left adrenal gland


title: U251 NC 3

value: Control


title: U251shA2B1 1


title: bone marrow, males born to Schistosoma mansoni chronically infected females, rep1, ADT and mRNA-derived combined cDNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT) was performed using the BD SevenBridges pipeline where and aligning to the mm10 genome build and Ensembl 93 annotations.
The Sevenbridges (The only processing system for BD Rhapsody) pipeline only generates a combined file that has both ADT and GEX.
Manufacturer-developed algorithms: recursive substation error correction (RSEC), distribution-based error correction (DBEC).
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10-3.0.0
Supplementary files format and content: BD Rhapsody Genomics output files: ReadsPerCell.csv, RSEC_MolsPerCell.csv, DBEC_ReadsPerCell.csv
Library strategy: CITE-seq

source_name: bone marrow

extract_protocol:
Femurs were harvested from pups 28-35 days old or females chronically infected with Schistosoma mansoni or age-matched control females. The end of the bone connected to the knee is cut, exposing bone marrow. Using a needle, a hole was punched into the bottom of a 200ul tube, and the bone is placed inside, cut side down, with 50ul of media. This tube was then placed in a 1.5mL tube and then spun at <10,000 RPM for 15 seconds at 4 degrees. Excess media was discarded, and cells were lysed with BD lysis buffer diluted to 1X for 30 seconds. The reaction was quenched using 1%FBS and cells were pelleted by centrifugation at 200xg for 5 minutes at 4 degrees. Primary antibody staining was done for 30 minutes in the dark at 4 degrees and washed twice before being filtered through a 40um filter and pooled. At least 3 mice were used per pool. Then the cells were sorted on a FACS Aria. After sorting, cells were stained with AbSeq antibodies per manufacture’s instruction. Cells were counted and resuspended at a concentration of 20,000 cells/ul before proceeding to library construction.
Library was prepared using BD Rhapsody library construction protocol (BD Biosciences). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the BD Rhapsody library construction protocol (BD Biosciences) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for BD Rhapsody library construction protocol (BD Biosciences). For antibody-derived tagged library, we used the protocol according to  BD Rhapsody library construction protocol (BD Biosciences)
-CITE-seq library: amplification was performed at 95°C for 5min followed by eight cycles at 95°C for 30s; 60°C for 30’s; 72°C for 30’s and final elongation 72°C for 1min.  Libraries were run on a BioAnalyzer to ensure proper amplification.

value: bone marrow

value: B cells and Hematopoietic Stem and Progenitor Cells (HSPCs)

value: male pups from S. masoni infected mothers

value: anti-CD117 (BD 940127), anti-CD16/32 (BD 940109), anti-Sca-1 (BD 940130), anti-CD138 (BD 940137), anti-CD124-PE- anti-PE (BD custom made), CD127-APC-anti-APC (BD custom made)


title: MUT-2

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the mouse reference genome hg38 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene.
Assembly: Differential expression was assessed by DESeq2 using read counts as input.
Supplementary files format and content: Hg38
Supplementary files format and content: tab-delimited text files include TPM values and annotations for each sample

growth_protocol: C4-2 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: M017AAB_T1_scR_CEL-Seq2_1

description:
CelSeq-2
Pretreatment NBL M017AAB_T1


title: MUT-3


title: bone marrow, males born to control females, rep1, ADT and mRNA-derived combined cDNA

value: male pups from control mothers


title: U251 NC 1

value: cell line

value: Glioma


title: bone marrow, non-infected (control) females, rep1, ADT and mRNA-derived combined cDNA

value: control mothers


title: CTRLMyoblasts,untreated, sample9 [CTRL_9]

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

country: Spain

institute: Universidad de Valencia

data_processing:
Trim Galore , version 0.6.6, Quality >30
STAR,  version 2.7.10a
RSEM, version 1.3.1
Assembly: GRCh38.p13
Supplementary files format and content: CSV of counts for each sample

source_name: Primary cell lines

extract_protocol:
Total RNA from human myoblasts was isolated using TriReagent following manufacturer’s recommendations. One microgram of RNA was digested with DNaseI and reverse-transcribed with SuperScript II Reverse Transcriptase using random hexanucleotides.
TruSeq Stranded mRNA Library prep kit (Illumina)

value: Primary cell lines

value: Myoblast


title: M017AAB_T1_scR_CEL-Seq2

description:
CelSeq-2
Pretreatment NBL M017AAB_T1

value: High-risk NBL

value: pre-treatment

value: female


title: U251 NC 2


title: bone marrow, Schistosoma mansoni chronically infected females, rep1, ADT and mRNA-derived combined cDNA

value: 8 weeks post S. masoni infection


title: WT-2

value: WT


title: opt3-2 rosettes Fe deficient rep2

city: Taipei

first: Louis

last: Grillet

address: Agricultural Chemistry Building No. 2, Rm. 209A No. 1, Sec. 4, Roosevelt Rd.

country: Taiwan

institute: National Taiwan University

data_processing:
Raw data consist of PF reads (Illumina chastity filter).
Demultiplex and base-calling was performed using bcl2fastq 1.8.4 with default settings.
Adapter removal was done using Trimmomatic 0.35 software in paired end mode (Keep-to-reads) with parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true CROP:151 MINLEN:75
Reads were mapped to the TAIR10 transcriptome using Bowtie 2.0.6 with parameters -k 30 --gbar 151, only read pairs mapping to the same transcripts were accepted
Rest reads were mapped to the TAIR10 genome using BLAT v34 with parameters -q=rna -t=dna -maxIntron=50000
Read counts and RPKM values of genes were computed using Rackj (http://rackj.sourceforge.net/)
Read counts of compared samples were normalized using the TMM method (edgeR 3.12.1) and the VOOM method (limma 3.26.9)
Normalized read counts were transformed into normalized RPKMs using EXCEL and compared using Z-TEST
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include TMM values for each sample and for each comparison.

organism: Arabidopsis thaliana

source_name: Roots of T-DNA insertional mutant line Salk_021168

growth_protocol: Plants were grown in vitro, horizontally in square Petri dishes, with light intensity of 50 Âµmol.m-2.s-1, continuous illumination, on ES media (Estelle and Somerville, 1987) containing 1.5% sucrose. Each plate contained 25 seedlings.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy plant Minikit. Quality of the samples was estimated with a Bioanalyzer 2100. RIN score ranged from 9.8 to 10 for root samples, and from 8.3 to 8.7 for leaves.
Libraries were prepared using the TruSeq stranded mRNA LT Sample Prep Kit following manufacturer's instruction.

treatment_protocol: Plants were grown for 10 days on full ES media, and transferred to plates containing either full ES media (control) or ES media without Fe and supplemented with 100 ÂµM FerroZine. Samples were collected 72 hours after transfer.

value: Whole rosettes

value: T-DNA insertion line Salk_021168

value: Fe-deficient media


title: WT-3


title: DM1Myoblasts, untreated,sample5 [DM1_5]


title: opt3-2 rosettes Fe deficient rep1


title: colon goblet cells [mouse] - [Epcam+, Cd44+, Kit+] - [replicate #3]

city: Nutley

first: Piero

last: Dalerba

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation (CDI)

institute: Hackensack Meridian Health

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ009

data_processing:
RNA-seq data was processed and mapped using OLego (Wu et al., Nucleic Acids Research, 41:5149–5163, 2013) and normalized using standard computational pipelines such as cufflinks (Trapnell et al., Bioinformatics, 25:1105-1111, 2009; Trapnell et al., Nature Protocols, 7:562-578, 2012). Mapping was performed onto the UCSC mm10 mouse genome. Gene-expression levels were quantified by computing Transcripts per Million (TPM) values. Computation of gene-level TPM values and retriveal of gene annotations were performed using the tximport and biomaRt software packages, implemented within the R software. A custom PYTHON script was used to organize the data. Finally, gene-expression levels were reported either as log2(TPM) values (when TPM>1), or as (TPM-1) values (when TPM=1 or TPM<1).
Assembly: Genome assembly: UCSC mm10
Supplementary files format and content: Tab-delimited text files report expression levels for each gene in each sample. Gene-expression levels are reported either as log2(TPM) values (when TPM>1), or as (TPM-1) values (when TPM=1 or TPM<1).

source_name: colon epithelial cells [mouse]

growth_protocol: Colon epithelial cells were purified from primary colonic tissues of adult female mice (strain: C57BL/6J; source: The Jackson Laboratory, stock #000664).

extract_protocol:
Sorted cells were centrifuged to form a pellet and flash-frozen in liquid nitrogen. Total RNA was extracted using the NuceloSpin RNA XS kit (Macherey-Nagel).
RNA-seq libraries were generated using the Illumina Stranded mRNA Prep kit, which employes poly-A oligonucleotides in order to "pull-down" mRNAs. RNA-seq libraries were sequenced using either an Illumina HiSeq 4000 machine (30 million, single-end, 100 bp reads) or an Illumina NovaSeq 6000 machine (20 million, paired-end, 100 bp reads). Individual samples are annotated with regard to the platform used to sequence them.

treatment_protocol: Whole epithelial crypts were detached from colon tissues using EDTA (5 mM) and then dissociated into single-cell suspensions using DNAse-I (100 units/ml) and Collagenase-III (200 units/ml). Single-cell suspensions were stained first with monoclonal antibodies (anti-Epcam FITC, clone G8.8, BioLegend; anti-Cd44-APC, clone IM7; BioLegend; anti-Kit-PE, clone 2B8, BioLegend; anti-Cd66a-APC/Cy7, clone Mab-CC1, BioLegend; anti-Cd3-PE/Cy5, clone 17A2, BD Biosciences; anti-Cd16/Cd32-biotin, clone 2.4G2, BD Biosciences; anti-Cd31-biotin, clone 390, eBioscience; anti-Cd45-biotin, clone 30F-11, BD Biosciences) and secondarily with Streptavidin-PE/Cy5 (BD Biosciences). Target epithelial populations (Epcam+/Cd44+/Kit-neg, Epcam+/Cd44+/Kit+, Epcam+/Cd44-neg/Cd66a-high) were sorted by FACS, after exclusion of dead cells (DAPI+), cell doublets (serial gating based on FSC-A vs. FSC-H and SSC-A vs. SSC-W profiles) and cells of non-epithelial lineages (Cd3+, Cd16/Cd32+, Cd31+, Cd45+), as previously published (Rothenberg et al., Gastroenterology, 142:1195-1205, 2012).

tag: strain

tag: cell phenotype

value: Epcam+, Cd44+, Kit+

value: enriched in goblet cells [bottom crypt]


title: M787AAA_T2_scR_CEL-Seq2_3

description:
CelSeq-2
Pretreatment NBL M787AAA_T2

value: NBL tumor left adrenal gland

value: CDK4 amplified


title: colon Lgr5+ cells [mouse] - [Epcam+, Cd44+, Kit-neg] - [replicate #3]

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ008

value: Epcam+, Cd44+, Kit-neg

value: enriched in Lgr5+ cells [bottom crypt]


title: opt3-2 rosettes control rep2

value: Control ES media


title: colon enterocytes [mouse] - [Epcam+, Cd44-neg, Cd66a-high] - [replicate #3]

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ007

value: Epcam+, Cd44-neg, Cd66a-high

value: enriched in enterocytes [top crypt]


title: MUT_H3K27ac

library_source: genomic

data_processing:
Libraries were quantified and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).
Reads mapped to the hg38 genomic using BWA were filtered by PICARD-MarkDuplicates (Galaxy Version 2.18.2.2), and the nonredundant reads were used for peak calling.
MACS2-callpeak (Galaxy Version 2.1.1.20160309.6) was used for performing peak calling with the threshold, FDR < 0.05.
bigWig files were generated using the bamCoverage.
ChIP peak profile plots and read-density heat maps were generated using deepTools, and cistrome overlap analyses were carried out using the ChIPseeker.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
The CUT&Tag assay was conducted using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903). Briefly, 105 C4-2 cells were collected and washed once with 500 μl wash buffer before they were bound to ConA beads for 10 min at 25 °C.
Then, cells were incubated with IgG, anti-AR (Abcam; ab108341), anti-FOXA1 (Proteintech; 20411-1-AP) and anti-H3K27ac (Cell Signaling Technology; 92964S) at 4 °C overnight. Anti-rabbit IgG was added and incubated for 1 h at 25 °C the next day. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G-Tnp for 1 h at 25 °C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tag mentation buffer and incubated at 37 °C for 1 h. Tag mentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55 °C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water.
Libraries were constructed using ‘TD903 Hyperactive Universal CUT&Tag Assay Kit for Illumina’ and ‘TD202 TruePrep Index Kit V2 for Illumina’ from Vazyme Biotech.

tag: chip antibody

value: H3K27ac, Abcam, Cat#:ab4729


title: opt3-2 rosettes control rep1


title: DM1Myoblasts, untreated,sample2 [DM1_2]

value: Primary cell lines

value: Myoblast


title: IMA3 OE rosettes Fe deficient rep2

source_name: Roots of transgenic plants transformed with the vector pH2GW7 into which the At2g30766 ORF was cloned

value: 35spro:IMA3 ORF


title: MUT-1


title: WT_H3K27ac

value: WT


title: WT-1


title: DM1Myoblasts, Treated23bV2, sample4, rep2 [DM1_4_2_23bV2]


title: DM1Myoblasts, Treated23bV2, sample4, rep1 [DM1_4_1_23bV2]


title: colon Lgr5+ cells [mouse] - [Epcam+, Cd44+, Kit-neg] - [replicate #2]

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ005

value: female


title: IMA3 OE rosettes Fe deficient rep1

value: Whole rosettes


title: MUT_AR

value: AR, Abcam, Cat#:ab108341


title: DM1Myoblasts, Treated23bV2, sample1, rep2 [DM1_1_2_23bV2]


title: IMA3 OE rosettes control rep2


title: DM1Myoblasts, Treated23bV2, sample1, rep1 [DM1_1_1_23bV2]


title: colon enterocytes [mouse] - [Epcam+, Cd44-neg, Cd66a-high] - [replicate #2]

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ004


title: WT_AR


title: IMA3 OE rosettes control rep1


title: bone marrow, males from uninfected mothers, rep1, V(D)J-derived cDNA

description: V(D)J/BCR

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, V(D)J and ADT) was performed using the 10x genomics Cell Ranger pipeline where ADT and V(D)J sequences were treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis) for mRNA and ADT. V(D)J was processed using scRepertoire.
Assembly: mm10-3.0.0
Supplementary files format and content: 10x Genomics output files:filtered_feature_bc_matrix.h5

extract_protocol:
Femurs were harvested from pups either born to S. mansoni infected mothers or uninfected mothers at 28-35 days old. The end of the bone connected to the knee is cut, exposing bone marrow. Using a needle, a hole was punched into the bottom of a 200ul tube, and the bone is placed inside, cut side down, with 50ul of media. This tube was then placed in a 1.5mL tube and then spun at <10,000 RPM for 15 seconds at 4 degrees. Excess media was discarded, and cells were lysed with BD lysis buffer diluted to 1X for 30 seconds. The reaction was quenched using 1%FBS and cells were pelleted by centrifugation at 200xg for 5 minutes at 4 degrees. Primary antibody staining was done for 30 minutes in the dark at 4 degrees and washed twice before being filtered through a 40um filter and pooled. At least 3 mice were used per pool. Then the cells were sorted on a FACS Aria. After sorting, cells were stained with TotalSeq antibodies per manufacture’s instruction. Cells were counted and resuspended at a concentration of 10,000 cells/ul before proceeding to library construction.
Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and amplified by PCR according to the Chromium Single Cell 5’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. For all cDNA library preparations, we further proceeded according to the manufacturer’s instructions for Single Cell 5’ v2 protocol (10x Genomics). mRNA and ADT sequences were combined in Cell Ranger, outputting one file per sample for those two libraries.
V(D)J library: Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics)
CITEseq library: Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics)

value: bone marrow

value: Immature and T1 B cells

value: Born to uninfected (control) mothers

value: Male


title: IMA1 OE rosettes Fe deficient rep2

source_name: Roots of transgenic plants transformed with the vector pH2GW7 into which the At1g47400 ORF was cloned

value: 35spro:IMA1 ORF

value: Fe-deficient media


title: DM1Myoblasts, Treated23bV2, sample3, rep2 [DM1_3_2_23bV2]


title: bone marrow, males from uninfected mothers, rep1, mRNA-derived cDNA

description: polyA RNA


title: bone marrow, males from uninfected mothers, rep1, ADT-derived cDNA

description: protein

value: (405747) TotalSeq™-C0571 anti-mouse IgD Antibody


title: MUT_ATAC

data_processing:
ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA and only uniquely mapped reads were kept,
Filtered bam files were used for peak calling by MACS2.
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Cells were collected and lysed to obtain purified nucleus; The Tn5 enzyme transposable reaction was carried out and the open regions of chromatin were fragmented; the fragmented DNA was purified; the purified DNA was amplified. The amplified DNA was sized to remove non-target fragments.
ATAC libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina kit.Purified fragmented DNA were amplified by PCR reaction,and the libraries were first purified by MinElute PCR purification column(Qiagen)and then further size-selected by VAHTS DNA Clean Beads to obtain libraries with a size distribution between 100 and 1500 bp.


title: IMA1 OE rosettes Fe deficient rep1


title: DM1Myoblasts, untreated,sample1 [DM1_1]


title: WT_ATAC


title: MUT_FOXA1

value: FOXA1, Proteintech, Cat#:20411-1-AP


title: DM1Myoblasts, Treated23bV2, sample3, rep1 [DM1_3_1_23bV2]


title: DM1Myoblasts, untreated,sample4 [DM1_4]


title: IMA1 OE rosettes control rep2

value: Control ES media


title: DM1Myoblasts, untreated,sample3 [DM1_3]


title: Primed OSKLH iPSC_4 (scRNA-seq)

city: San Francisco

first: Akira

last: Kunitomi

state: CA

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description: Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

data_processing:
Raw sequencing data was converted to the standard FASTQ files by executing cellranger mkfastq (3.1.1, 10x Genomics)
Gene counts of each sample were generated by executing cellranger count (3.1.1, 10x Genomics) with refdata-cellranger-GRCh38-3.0.0 as the reference dataset.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

growth_protocol: HDFs were maintained in fibroblast medium, and Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates.

extract_protocol:
mRNA was extracted according to the manufacturer's protocol.
RNA libraries were prepared according to the manufacturer’s protocol using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v3 and Single Index Kit.

value: Primed induced pluripotent stem cells

tag: gender

value: Female


title: WT_FOXA1


title: EYFP OE rosettes Fe deficient rep2

source_name: Roots of transgenic plants transformed with the vector pH2GW7 into which the EYFP ORF was cloned

value: 35spro:EYFP (transgenic control)


title: bone marrow, females from uninfected mothers, rep1, V(D)J-derived cDNA

description: V(D)J/BCR


title: bone marrow, males from infected mothers, rep1, V(D)J-derived cDNA

description: V(D)J/BCR

value: Born to S. mansoni infected mothers


title: bone marrow, females from uninfected mothers, rep1, ADT-derived cDNA

description: protein


title: EYFP OE rosettes Fe deficient rep1


title: EYFP OE rosettes control rep2


title: DM1Myoblasts, Treated23bV2, sample2, rep2 [DM1_2_2_23bV2]

value: Primary cell lines

value: Myoblast


title: bone marrow, females from uninfected mothers, rep1, mRNA-derived cDNA

description: polyA RNA


title: OSKLH_day15 (scRNA-seq)

description: Human dermal fibroblasts sampled at day15 after infection with SeV-OSKLH

value: Human dermal fibroblasts

value: infection with SeV-OSKLH


title: bone marrow, females from infected mothers, rep1, mRNA-derived cDNA

description: polyA RNA

value: bone marrow


title: OSKLH_day5 (scRNA-seq)

description: Human dermal fibroblasts sampled at day5 after infection with SeV-OSKLH


title: bone marrow, females from infected mothers, rep1, ADT-derived cDNA

description: protein

value: Immature and T1 B cells


title: CTRLMyoblasts,untreated, sample3 [CTRL_3]

value: Control


title: opt3-2 roots Fe deficient rep2

value: Roots

value: T-DNA insertion line Salk_021168


title: IMA1 OE rosettes control rep1

value: Whole rosettes

value: 35spro:IMA1 ORF


title: Primed OSKLH iPSC_3 (scRNA-seq)

source_name: Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed OSKLH iPSC_1 (scRNA-seq)


title: Primed OSKLH iPSC_2 (scRNA-seq)


title: DM1Myoblasts, untreated,sample7 [DM1_7]


title: EYFP OE rosettes control rep1


title: bone marrow, females from infected mothers, rep1, V(D)J-derived cDNA

description: V(D)J/BCR


title: AT2, Input, sample 1

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Raw reads were aligned to mm10 using bwa (parameters ‘-q 5 -l 32 -k 2’). Duplicates were removed with Picard tools, and the samples were downsampled to 43 million (AT1) or 48.8 million (AT2) reads using samtools.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Lung, adult Sftpc-EGFP

extract_protocol:
Target cells were FACS sorted and were crosslinked by 1% formaldehyde for 10 min. Glycine was then added to quench aldehyde. The cell pellets were stored at -80°C until library preparation.
Crude nuclei were isolated and were sonicated by using a Covaris S220 sonicator. LB1 antibodies (Abcam, ab16048) were added and the mixture was incubated 4°C overnight. Libraries were prepared with NEBNext Ultra II DNA library prep kit (NEB).

value: Lung, adult Sftpc-EGFP

value: Alveolar type 2 cell

value: LB1 (abcam, ab16048)


title: DM1Myoblasts, Treated23bV2, sample7, rep1 [DM1_7_1_23bV2]


title: Primed OSKL iPSC_4 (scRNA-seq)

value: Primed induced pluripotent stem cells

value: Female


title: Primed OSKL iPSC_2 (scRNA-seq)


title: opt3-2 roots control rep1

value: Control ES media


title: AT2, LB1, sample 2


title: CTRLMyoblasts,untreated, sample2 [CTRL_2]

value: Primary cell lines


title: CTRLMyoblasts,untreated, sample4 [CTRL_4]

value: Myoblast


title: AT2, Input, sample 2


title: Primed OSKL iPSC_1 (scRNA-seq)


title: DM1Myoblasts, Treated23bV2, sample6, rep2 [DM1_6_2_23bV2]


title: opt3-2 roots Fe deficient rep1

value: Fe-deficient media


title: IMA3 OE roots Fe deficient rep2

value: 35spro:IMA3 ORF


title: CTRLMyoblasts,untreated, sample1 [CTRL_1]


title: Primed OSKL iPSC_3 (scRNA-seq)


title: DM1Myoblasts, Treated23bV2, sample6, rep1 [DM1_6_1_23bV2]


title: OSKL_day15 (scRNA-seq)

description: Human dermal fibroblasts sampled at day15 after infection with SeV-OSKL

value: Human dermal fibroblasts


title: AT1, Input, sample 2

source_name: Lung, adult Hopx-EGFP

value: Lung, adult Hopx-EGFP

value: Alveolar type 1 cell


title: DM1Myoblasts, Treated23bV2, sample8, rep2 [DM1_8_2_23bV2]


title: IMA3 OE roots Fe deficient rep1

value: Roots


title: AT1, Input, sample 1


title: IMA3 OE roots control rep2


title: OSKL_day5 (scRNA-seq)

description: Human dermal fibroblasts sampled at day5 after infection with SeV-OSKL


title: HDF (scRNA-seq)

description: Human dermal fibroblasts

source_name: Human dermal fibroblasts


title: opt3-2 roots control rep2

value: T-DNA insertion line Salk_021168


title: AT1, LB1, sample 2


title: AT2, LB1, sample 1


title: OSKLH_day15

data_processing:
Raw sequencing data was converted to the standard FASTQ files by executing cellranger-atac mkfastq (1.1.0, 10x Genomics).
Fastq files from single cell ATAC-seq were mapped by CellRanger using the hg38 reference (refdata-cellranger-atac-GRCh38-1.2.0).
Mapping was performed using cellranger-atac count function by pool and then the data aggregated by cellranger-atac aggr function.
Assembly: GRCh38
Supplementary files format and content: Fragments data in tab separated txt (.tsv)

source_name: Human dermal fibroblasts sampled at day15 after infection with SeV-OSKLH

extract_protocol:
DNA was extracted according to the manufacturer's protocol.
The libraries were prepared according to the manufacturer’s protocol using the 10x Genomics Chromium Single Cell ATAC Reagent Kit v1

value: infection with SeV-OSKLH


title: DM1Myoblasts, untreated,sample6 [DM1_6]


title: AT1, LB1, sample 1


title: DM1Myoblasts, Treated23bV2, sample8, rep1 [DM1_8_1_23bV2]


title: CTRLMyoblasts,untreated, sample7 [CTRL_7]

value: Control


title: OSKLH_day2

description: Human dermal fibroblasts sampled at day2 after infection with SeV-OSKLH


title: OSKLH_day5

source_name: Human dermal fibroblasts sampled at day5 after infection with SeV-OSKLH


title: AT1_Cdc42 knockout, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the STARSolo 2.7.9a and downstrema analysis perfimed using Seurat v4
Assembly: mm39

source_name: Lung

extract_protocol:
Target cells were FACS sorted and were loaded onto the 10x Chromium (10X Genomics) aiming for 10,000 cells per sample.
Libraries were prepared according to the manufacturer’s protocol using Chromium Single Cell 3’ v2 chemistry.

value: Epithelial cells  Epithelial cells  Epithelial cells

value: Lung

value: Hopx-creERT2; Cdc42 fl/fl; R26R_EYFP

tag: age

value: 8-10 weeks old


title: Left bronchial ligation, scRNAseq

description: 10x Genomics

value: Hopx-creERT2; R26R_EYFP

value: 14-16 weeks old


title: DM1Myoblasts, Treated23bV2, sample2, rep1 [DM1_2_1_23bV2]

value: Primary cell lines


title: Wildtype, scRNAseq

description: 10x Genomics


title: IMA1 OE roots Fe deficient rep1

value: 35spro:IMA1 ORF


title: IMA1 OE roots control rep1

value: Control ES media


title: CTRLMyoblasts,untreated, sample8 [CTRL_8]

value: Myoblast


title: IMA1 OE roots Fe deficient rep2

value: Fe-deficient media


title: EYFP OE roots Fe deficient rep2

value: 35spro:EYFP (transgenic control)


title: Pool_6_Infected_mom_female_2_GEX

description: bone marrow, females from infected mothers, rep2, mRNA-derived cDNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT) was performed using the 10x genomics Cell Ranger pipeline where ADT sequences were concatenated and treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10-3.0.0
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz (generated from both ADT and GEX data, and linked to the corresponding ADT sample records).

extract_protocol:
Femurs were harvested from pups either born to S. mansoni infected mothers or uninfected mothers at 28-35 days old. The end of the bone connected to the knee is cut, exposing bone marrow. Using a needle, a hole was punched into the bottom of a 200ul tube, and the bone is placed inside, cut side down, with 50ul of media. This tube was then placed in a 1.5mL tube and then spun at <10,000 RPM for 15 seconds at 4 degrees. Excess media was discarded, and cells were lysed with BD lysis buffer diluted to 1X for 30 seconds. The reaction was quenched using 1%FBS and cells were pelleted by centrifugation at 200xg for 5 minutes at 4 degrees. Primary antibody staining was done for 30 minutes in the dark at 4 degrees and washed twice before being filtered through a 40um filter and pooled. At least 3 mice were used per pool. Then the cells were sorted on a FACS Aria. After sorting, cells were stained with TotalSeq antibodies per manufacture’s instruction. Cells were counted and resuspended at a concentration of 10,000 cells/ul before proceeding to library construction.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. For the mRNA derived and antibody-derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v3.1 protocol (10x Genomics). ADT and mRNA sequencing files were pooled together by Cell Ranger.
-CITE-seq library: amplification was performed at 98°C for 45s followed by ten cycles at 95°C for 20s; 54°C for 30’s; 72°C for 20’s and final elongation 72°C for 1min.  Libraries were run on a BioAnalyzer to ensure proper amplification.

value: bone marrow

value: B cells and Hematopoietic Stem and Progenitor Cells (HSPCs)

value: female

value: Born to S. mansoni infected mothers


title: Pool_6_Infected_mom_female_2_ADT

description: bone marrow, females from infected mothers, rep2, ADT-derived cDNA

library_source: other

molecule: protein

value: TotalSeq™-B0012 anti-mouse CD117 (c-Kit) Antibody, TotalSeq™-B0130 anti-mouse Ly-6A/E (Sca-1) Antibody


title: OSKL_day15

source_name: Human dermal fibroblasts sampled at day15 after infection with SeV-OSKL

value: Human dermal fibroblasts

value: Female

value: infection with SeV-OSKL


title: colon goblet cells [mouse] - [Epcam+, Cd44+, Kit+] - [replicate #2]

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ006

value: Epcam+, Cd44+, Kit+

value: enriched in goblet cells [bottom crypt]


title: IMA3 OE roots control rep1

value: Roots

value: 35spro:IMA3 ORF


title: OSKL_day5

source_name: Human dermal fibroblasts sampled at day5 after infection with SeV-OSKL


title: DM1Myoblasts, untreated,sample8 [DM1_8]

value: Primary cell lines


title: IMA1 OE roots control rep2

value: 35spro:IMA1 ORF

value: Control ES media


title: OSKL_day2

description: Human dermal fibroblasts sampled at day2 after infection with SeV-OSKL


title: EYFP OE roots Fe deficient rep1

value: Fe-deficient media


title: CTRLMyoblasts,untreated, sample6 [CTRL_6]

value: Myoblast

value: Control


title: HDF

description: Human dermal fibroblasts


title: Pool_4_Infected_mom_female_1_GEX

description: bone marrow, females from infected mothers, rep1, mrna-derived cDNA

value: bone marrow

value: B cells and Hematopoietic Stem and Progenitor Cells (HSPCs)


title: DM1Myoblasts, Treated23bV2, sample5, rep1 [DM1_5_1_23bV2]


title: EYFP OE roots control rep2

value: 35spro:EYFP (transgenic control)


title: DM1Myoblasts, Treated23bV2, sample5, rep2 [DM1_5_2_23bV2]


title: Pool_4_Infected_mom_female_1_ADT

description: bone marrow, females from infected mothers, rep1, ADT-derived cDNA

value: female

value: Born to S. mansoni infected mothers

value: TotalSeq™-B0012 anti-mouse CD117 (c-Kit) Antibody, TotalSeq™-B0130 anti-mouse Ly-6A/E (Sca-1) Antibody


title: EYFP OE roots control rep1


title: Naive OSKLH iPSC_6 (bulkRNA-seq)

description: Naive induced pluripotent stem cells derived from  adult periferal blood mononuclear cells

data_processing:
FASTQ files were generated from bcl files using bcl2fastq v2.17.1.14 (illumina) and processed using ENCODE long-rna-seq-pipeline v2.3.4.
Sequenced reads were mapped to the human reference genome (GRCh38) using TopHat 2.1.1 or STAR 2.5.1b with GENCODE v24 gene annotations.
Normalized gene expression data was calculated using RSEM 1.2.23.
Gene count data was obtained using featureCounts bundled in Subread 1.5.1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

growth_protocol: Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö+Y medium.

extract_protocol:
mRNA or total RNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Naive induced pluripotent stem cells

value: Female


title: Naive OSKLH iPSC_5 (bulkRNA-seq)

description: Naive induced pluripotent stem cells derived from adult periferal blood mononuclear cells


title: CTRLMyoblasts,untreated, sample5 [CTRL_5]


title: Pool_5_Infected_mom_male_2_ADT

description: bone marrow, males from infected mothers, rep1, ADT-derived cDNA

value: male


title: 8175_3_Trans

city: Nanjing

first: Huichen

last: Song

state: Jiangsu

address: Qixia District, Xianlin Road No.163

institute: Nanjing university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: mouse

value: Diet-induced obese mice


title: HK-2  Yap/Taz-5h-replicate3

city: Hong  Kong

first: YANG

last: LIU

address: Lo Kwee-Seong Integrated Biomedical Sciences  Building, Area 39

department: School of Biomedical Sciences

institute: The Chinese University of Hong  Kong

data_processing:
Split the sequencing data into fastq files using the default parameters of bcl2fastq.
Remove the contaminated reads for adapters by using fastp
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2  v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TaKaRa MiniBEST Universal RNA Extraction Kit.1g of total RNA was used for the construction of sequencing libraries.
RNA libraries for sequencing were prepared using NEBNext Ultra RNA Library Prep Kit(Catalog #:E7530L) according to the manufacter's protocols

value: Human proximal tubular cell

value: electrotransfection with Yap and Taz plasmids


title: Pool_5_Infected_mom_male_2_GEX

description: bone marrow, males from infected mothers, rep1, mRNA-derived cDNA

source_name: bone marrow


title: 8175_2_Trans


title: HK-2  Yap/Taz-5h-replicate2


title: Pool_2_Uninfected_momminusfemale_GEX

description: bone marrow, females from uninfected mothers, rep1, mRNA-derived cDNA

value: Born to uninfected (control) mothers


title: Pool_1_Uninfected_momminus_male_GEX

description: bone marrow, males from uninfected mothers, rep1, mRNA-derived cDNA


title: NC_2

value: NC control


title: NC_3


title: HK-2  Yap/Taz-replicate1


title: Naive OSKLH iPSC_2 (bulkRNA-seq)

description: Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: 8175_1_Trans


title: Naive OSKLH iPSC_4 (bulkRNA-seq)

source_name: Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Naive OSKLH iPSC_1 (bulkRNA-seq)


title: Pool_2_Uninfected_momminusfemale_ADT

description: bone marrow, females from uninfected mothers, rep1, ADT-derived cDNA


title: HK-2 GFP-5h-replicate3

value: electrotransfection with GFP plasmids


title: HK-2 GFP-5h-replicate2


title: Naive OSKL iPSC_6 (bulkRNA-seq)

source_name: Naive induced pluripotent stem cells derived from  adult periferal blood mononuclear cells


title: NC_1


title: H9_ESC

description: Human primed embryonic stem cells

source_name: Human primed embryonic stem cells

value: Human embryonic stem cells


title: Day 7 (3): 7 days post infection dermal macrophages rep3

first: Aaron

middle: James

last: Forde

address: Breisacher Str. 115

institute: Medical Center University of Freiburg

data_processing:
De-multiplexing: Illumina bcl2fastq
Trimming: Cutadapt
Read count: STAR (V2.5.2b)
Quality control reads: FASTQC
Alignment: STAR (V2.5.2b)
Differentially expressed genes: DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tabular files of normalized_reads in control, bystanding and CMV-infected alveolar macrophages

source_name: CD64hi Dermal Macrophage

extract_protocol:
Total RNA, obtained with QIAGEN microkit, was subjected to library synthesis.
After the QC procedures, total mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: WT mice were injected intradermally with S. aureus (strain Newman) in both ears or left uninfected. CD64hi dermal macrophages were sorted from the tissue 1 day, 5 days or 7 days after infection.

value: Wild Type

value: Dermis

value: CD64hi Dermal Macrophage

value: 7 days post infection


title: DM1Myoblasts, Treated23bV2, sample7, rep2 [DM1_7_2_23bV2]

source_name: Primary cell lines

value: Primary cell lines

value: Myoblast


title: HK-2 GFP-5h-replicate1


title: Day 7 (1): 7 days post infection dermal macrophages rep1


title: Day 7 (2): 7 days post infection dermal macrophages rep2


title: Naive OSKLH iPSC_3 (bulkRNA-seq)

value: Naive induced pluripotent stem cells


title: Naive OSKL iPSC_4 (bulkRNA-seq)

value: Female


title: M18, Tail Vertebrae, scRNAseq

city: Fontenay-aux-Roses

first: Julien

last: Calvo

address: 18, route du panorama

department: Institut de Radiobiologie Cellulaire et Moléculaire

country: France

institute: Commissariat à l'Energie Atomique

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Seurat v4
Assembly: hg18
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tail Vertebrae

extract_protocol:
Femur, Thoracic and Tail vertebrae of xenograft NSG mice were crushed with PBS to recovered cells from bone marrow. human T-ALL cells were purified after labeling with anti-human CD45 PE conjugated antibody followed by immuno magnetic selection with anti-Phycoerythrin (PE) microbeads (Miltenyi Biotech). Purifications were analyzed by flow cytometry then resuspended in PBS supplemented with 0.04% BSA.
Leukemic cells are counted with trypan blue then suspended at 1 x 106 cells/mL in PBS 0.04% BSA. 20 000 cells per condition were loaded in Chromium Next GEM Chip G. Single-cell libraries were generated using Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1): GEM, Library and Gel Bead Kit v3.1 (PN-1000128), Chip G Single Cell kit (PN-1000127) and Dual Index kit TT Set A (PN-1000215) (10x Genomics), and following the Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1) User Guide (manual part no. CG0000204 Rev D). Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. Amplified cDNA and libraries were verified on Bioanalyzer 2100 (Agilent Technologies) using High Sensitivity DNA kit (Agilent Technologies). During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample dual index were added.

value: human Leukemic cells

value: Tail Vertebrae

value: NOD.Cg-Prkdcscid Il2rgtm1WjI/SzJ

value: 6-8 weeks old


title: Naive OSKL iPSC_3 (bulkRNA-seq)


title: M18, Thoracic Vertebrae, scRNAseq

description: 10x Genomics

source_name: Thoracic Vertebrae

value: Thoracic Vertebrae


title: Day 5 (2): 5 days post infection dermal macrophages rep2

value: 5 days post infection


title: 8175_6

value: mouse hepatocarcinoma cells


title: Day 5 (3): 5 days post infection dermal macrophages rep3


title: Naive OSKL iPSC_1 (bulkRNA-seq)


title: Naive OSKL iPSC_2 (bulkRNA-seq)


title: Pool_1_Uninfected_momminus_male_ADT

description: bone marrow, males from uninfected mothers, rep1, ADT-derived cDNA

value: bone marrow

value: B cells and Hematopoietic Stem and Progenitor Cells (HSPCs)

value: male

value: Born to uninfected (control) mothers

value: TotalSeq™-B0012 anti-mouse CD117 (c-Kit) Antibody, TotalSeq™-B0130 anti-mouse Ly-6A/E (Sca-1) Antibody


title: 8175_4


title: 8175_1


title: Day 5 (1): 5 days post infection dermal macrophages rep1

value: Wild Type

value: Dermis

value: CD64hi Dermal Macrophage


title: Naive H9 ESC (bulkRNA-seq)

description: Naive embryonic stem cells which were reset from the primed to naive state

value: Naive embryonic stem cells


title: MCF10A cells, PyST degradation R2

city: Boston

first: Cherubin

last: Manokaran

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
Basecalls were performed using Illumina CASAVA 1.8
Raw reads containing adapters, base quality scores less than 5 and more than ten percent N’s were removed using Cutadapt v1.16.
Transcript-level counts were quantified from the processed reads using Kallisto v0.46 and the hg19 transcriptome and summarized to the gene-level. Differential expression was determined using DESeq2.
For validation, processed reads were also mapped to hg19 with STAR v2.7.3a 2-pass alignment using ENCODE parameters, first with a genome index of 100 bp overhangs and then with an index built using 75 bp overhangs and a combination of the junctions determined from the initial alignments. Unstranded gene hits were counted for both alignments using HTSeq v0.9.1 with a minimum alignment quality of 10, and differential expression determined in DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include transcript counts and abundances for each sample

extract_protocol:
Total RNA was purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, #T2010). On-column DNase digestion was performed to remove any residual DNA. The integrity of total RNA was assessed by an Agilent Bioanalyzer 2100 at Novogene.
The cDNA library was constructed using NEBNext® Ultra™ II RNA Library Prep with Sample Purification Beads (New England Biolabs, #E7775). Briefly, a total of 400 ng RNA per sample was subjected to poly(A)-selection, followed by reverse transcription to generate cDNA. The resulting cDNA was subjected to adapter ligation and PCR amplification. Library quality control was performed using Labchip and qPCR.Sequencing was then performed on an Illumina Novaseq 6000 to generate 150 bp paired-end reads (Novogene).

value: mammary epithelial cells

value: PyST-FKBP12 (F36V)

tag: time

value: 22 hours


title: 8175_2

tag: cell line


title: MCF10A cells, PyST degradation R1

tag: cell type


title: Stem cells- and tuft-derived organoids [LX235_LX236]

city: Utrecht

first: Amir

last: Giladi

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
cellranger
Recovered cellplex barcodes were used to assign single cells to experimental batches. Single cells with less than 64 UMI of a specific cellplex barcodes were discarded from down-stream analysis. Single cells with less than 8-fold UMI count ratio between highest and second highest cellplex barcodes were marked as doublets and discarded from down-stream analysis. Single cells with less than 1,000 genomic UMIs or more than 20% mitochondrial content failed to pass QC and were discarded from further analysis, resulting in 11,550 QC-positive cells.
Assembly: hg38
Supplementary files format and content: Genes x cells tab delimited table
Supplementary files format and content: A metadata file containing relevant information (experiment condition, etc.) for each sequenced cell
Supplementary files format and content: Matrix file containing number of detected transcripts per feature and cell
Supplementary files format and content: A features file (either gene or Cellplex barcode)
Supplementary files format and content: A barcodes (cells) file

source_name: Ileum-derived organoids

growth_protocol: Human intestinal organoids were split once a week by mechanic dissociation. In this study, basic culture medium includes advanced Dulbecco’s modified Eagle’s medium/F12 (Gibco) supplemented with 100 U/ml penicillin/streptomycin (Gibco), 10 mM HEPES (Gibco), 1× Glutamax (Gibco), 1× B-27 Supplement (Life Technologies), 1.25 mM N-acetylcysteine (Sigma-Aldrich) and 1% (v/v) recombinant Noggin (U-Protein Express).

extract_protocol:
Chromium Next GEM Single Cell 3’ v 3.1 platform
Organoids were dissociated into single cells using TrypLE (TrypLE Express, Life Technologies) with 10 μM Rho kinase inhibitor (Abmole) in 37°C and mechanical disruption by pipetting every 5 minutes.

treatment_protocol: Organoids were expanded in human expansion medium as described before. For differentiation toward tuft cells, organoids were washed 30 minutes in DMEM+++ at day 4 and the medium is replaced for tuft cell differentiation medium (diff): 0.5 nM Wnt surrogate (U-Protein Express), 20% (v/v) R-spondin1 (condition medium), 50 ng/ml recombinant human EGF (Peprotech), 10 μM Notch inhibitor DAPT (Sigma-Aldrich) in basic culture medium. For tuft cell differentiation with IL-4 and IL-13, EGF was withdrawn, 5 ng/ml human IL-4 (Peprotech) and 5 ng/ml human IL-13 (Peprotech) were supplemented to tuft cell differentiation medium (diff).

value: Ileum-derived organoids

value: CMO309,CMO301,CMO302 - organoids derived from stem cells, CMO310, CMO311, CMO312 - organoids derived from tuft cells

value: All cells

tag: genotype

value: CMO309, CMO312 expansion medium; CMO310, CMO301 differentiation medium; CMO311, CMO302 differentiation medium with IL-4/IL-13 supplementation

tag: patient age

value: adult


title: Day 1 (3): 1 day post infection dermal macrophages rep3

tag: tissue

value: 1 day post infection


title: TR149_340_IRP2_+/+_ZT5_Rep3_totalRNA

city: Lausanne

first: Hima

middle: Priyanka

last: Nadimpalli

address: Génopode Building, Room 500

country: Switzerland

institute: UNIL - CIG

data_processing:
Read adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were trimmed using cutadapt (v 3.5) with the following options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30 and reads were quality filtered using fastx_toolkit (-Q33 -q 30 -p 90).
Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA.
Reads were then mapped to rRNA and tRNA databases to remove contaminants using bowtie2 (-p 2 -L 15 -k 20 --no-unal -q).
Only reads that did not map to the above databases were mapped to mouse genome v38.100 using STAR (version 2.70f).
Assembly: mouse genome v38.100

extract_protocol:
For ribosome profiling, frozen liver tissues from individual mice were homogenized with 5-6 strokes using a Teflon homogenizer in 3 volumes of polysome buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, complete EDTA-free protease inhibitors (Roche) and 40 U/ml RNasin plus (Promega)) supplemented with 1% Triton X-100 and 0.5% Na deoxycholate. Liver lysates were incubated on ice for 10 min and cleared by centrifugation at 10000g, 4°C for 10 min. For each sample, 15 OD260 of liver lysate was digested with RNase I (Ambion) for 45 min at RT under gentle agitation and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Libraries from ribosome-protected fragments (RPF) and total RNA were prepared as described in Janich et al., 2015 with few modifications. 1 µg of RPF and total RNA samples were depleted of ribosomal RNA using RiboCop rRNA depletion kit V1.3 (Lexogen). Subsequent steps were performed according to Illumina TruSeq Ribo-Profile protocol.

value: liver

value: WT


title: 201B7 (bulkRNA-seq)

description: Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

value: Primed induced pluripotent stem cells

value: Female


title: 8175_3

value: mouse hepatocarcinoma cells


title: Naive OSKL iPSC_5 (bulkRNA-seq)

source_name: Naive induced pluripotent stem cells derived from adult periferal blood mononuclear cells

value: Naive induced pluripotent stem cells


title: TR148_340_IRP2_ko/ko_ZT5_Rep3_totalRNA

value: IRP2 knockout


title: KhES1 (bulkRNA-seq)

description: Primed embryonic stem cells

source_name: Primed embryonic stem cells

value: Primed embryonic stem cells


title: Day 1 (2): 1 day post infection dermal macrophages rep2

value: Wild Type

value: Dermis

value: CD64hi Dermal Macrophage


title: 8175_5


title: TR147_340_IRP2_+/+_ZT5_Rep2_totalRNA


title: Control (3): Control dermal macrophages rep3

value: Uninfected Contol


title: Primed OSKLH iPSC_8 (bulkRNA-seq)

source_name: Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: TR148_347_IRP2_ko/ko_ZT5_Rep3_totalRNA


title: Primed OSKLH iPSC_6 (bulkRNA-seq)


title: TR145_347_IRP2_+/+_ZT5_Rep1_totalRNA


title: M18, Femur, scRNAseq

description: 10x Genomics

source_name: Femur

value: human Leukemic cells

value: Femur

value: NOD.Cg-Prkdcscid Il2rgtm1WjI/SzJ

value: 6-8 weeks old


title: Day 1 (1): 1 day post infection dermal macrophages rep1

value: 1 day post infection


title: MCF10A cells, PyST R2

value: mammary epithelial cells

value: PyST-FKBP12 (F36V)

tag: treatment

value: vehicle (0.02 % DMSO v/v)

value: 22 hours


title: MCF10A cells, PyST R1


title: Primed OSKLH iPSC_5 (bulkRNA-seq)

value: Primed induced pluripotent stem cells

value: Female


title: Primed H9 ESC (bulkRNA-seq)

description: Primed embryonic stem cells


title: MCF10A cells, Control R2

value: WT

value: untreated


title: Control (2): Control dermal macrophages rep2

value: Wild Type


title: TR146_340_IRP2_ko/ko_ZT5_Rep2_totalRNA

value: liver

value: IRP2 knockout


title: Sc BY4741 pex3, Oac, biol rep 1

city: Groningen

first: Marc Pilegaard

last: Pedersen

address: Nijenborgh 7

institute: University of Groningen

data_processing:
Raw sequencing data is processed using fastp software (v0.20.0) to remove poor quality bases (below Phred Quality 20), remove adapters from the reads, remove shorter reads which are <30bp length
Raw sequencing data is processed using fastp software (v0.20.0) to remove remove adapters from the reads
Raw sequencing data is processed using fastp software (v0.20.0) to remove reads which are <30bp length
High quality sequence reads are aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference) v2.7.3a
Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool v1.3.3
Genes with less than 10 reads on an average across the compared groups were removed
Assembly: R64
Supplementary files format and content: NG-28902_alignment_index_files.tar.gz: archive containing results of the read mapping in BAM format
Supplementary files format and content: NG-28902_gene_counts.tar.gz: archive containing sample wise raw and normalized counts
Supplementary files format and content: R_counts_T1_cleaned.csv: genes with less than 10 reads on an average across the compared groups
Supplementary files format and content: NG-28902_gene_foldchanges.tar.gz: archive containing the sample wise comparison foldchange and significant foldchange values

organism: Saccharomyces cerevisiae BY4741

source_name: Euroscarf #Y03688

growth_protocol: Wake up cultures of S. cerevisiae were cultivated on mineral medium (Van Dijken et al., 1976) containing 0,5% glucose overnight, shifted to glucose media again in the morning, and followed by two dilutions into mineral medium  containing 0,5% acetate to ensure full depletion of residual glucose and acetate induced derepression. Upon reaching an optical density (660nm) of 0,5 in the second growth cycle on acetate, the cells were harvested. All cultivation procedures was performed as batch in shake flasks at 30 degrees Celsius.

extract_protocol:
RNA isolation, quantification and quality control was performed by Eurofins Genomics according to in-house protocols (Eurofins Genomics Germany GmbH, Project no: NG-28902)
Strand-specific cDNA library: The mRNA was poly-A purified and fragmented, followed by random primed cDNA library synthesis, adapter ligation and adapter specific PCR amplification.

treatment_protocol: The yeast cultures were flash cooled on wet ice and yeast pellets were collected by centrifugation (precooled). The collected pellets were treated with RNAlater® (Sigma, #R0901) according to the instructions of the manufacturer and the whole yeast pellets were flash frozen in liquid nitrogen, stored at -80 degrees Celsius and shipped for analysis on dry-ice. Experiments were conducted in biological triplicate.

value: Euroscarf #Y03688

value: MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0 pex3(YDR329c)::kanMX4

value: [delta]pex3, deletion strain

tag: sample type

value: Variable for biol rep 1


title: Sc BY4741 WT, Oac, biol rep 3

source_name: Euroscarf #Y00000

value: Euroscarf #Y00000

value: MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0

value: Wild type

value: Reference strain for biol rep 3


title: Primed OSKLH iPSC_3 (bulkRNA-seq)


title: MCF10A cells, Control R1

value: mammary epithelial cells


title: Sc BY4741 pex3, Oac, biol rep 3

value: Variable for biol rep 3


title: Primed OSKLH iPSC_7 (bulkRNA-seq)

value: Primed induced pluripotent stem cells


title: TR145_340_IRP2_+/+_ZT5_Rep1_totalRNA


title: Sc BY4741 pex3, Oac, biol rep 2

value: Variable for biol rep 2


title: Primed OSKLH iPSC_4 (bulkRNA-seq)

value: Female


title: TR144_347_IRP2_ko/ko_ZT5_Rep1_totalRNA


title: TR144_340_IRP2_ko/ko_ZT5_Rep1_totalRNA


title: Primed OSKLH iPSC_2 (bulkRNA-seq)


title: TR135_340_IRP2_+/+_ZT12_Rep3_totalRNA

value: WT


title: Sc BY4741 WT, Oac, biol rep 2

value: Reference strain for biol rep 2


title: C2C12 cells, ShPkm2, 48 h diff, rep1

city: Worcester

first: Tapan

last: Sharma

state: MA

address: 368 Plantation Street

department: Gene Therapy Centre

institute: University of Massachusetts Medical School

data_processing:
Libraries were sequenced using the BGIseq platform, averagely generating about 4.60 Gb bases per sample. Reads were filtered to remove adaptor-polluted, low quality and high content of unknown base reads.
About 79.80% of the raw reads were identified as clean reads. Of these, about 79.80% reads were mapped to genome with approximately 47.6% reads uniquely mapped to mouse reference genome mm10 using HISAT.
Transcripts were reconstructed using StringTie, and novel transcripts were identified using Cuffcompare. All transcripts were then combined together and mapped to the mm10 reference transcriptome using Bowtie.
Gene expression levels were calculated using RSEM. DEseq2 algorithm was used to detect differentially expressed genes (DEG).
Assembly: mm10
Supplementary files format and content: Tab-delimited file with fpkm, tpm, and raw counts

source_name: Immortalized cell line

growth_protocol: The C2C12 were maintained at sub-confluent densities in proliferation media containing Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS, Gibco), 1% penicillin-streptomycin in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Cells were harvested 48h after inducing differentiation. The total RNA was obtained with TRIzol-chloroform phase separation followed by iso-propanol precipitation. The total RNA pellet was resuspended in nuclease-free water.
RNA libraries were prepared by BGI Americas according to their standard protocol.

treatment_protocol: To induce myoblast differentiation, C2C12 cells were cultured in DMEM media supplemented with 2% Horse Serum (HS, Gibco), Insulin-Transferrin-Selenium-A (Gibco) and 1% penicillin-streptomycin in a humidified incubator at 37 °C with 5% CO2.

value: Immortalized cell line

value: Myoblasts

value: Pkm2 Knockdown

value: Myoblasts differentiation (48 h)


title: Control (1): Control dermal macrophages rep1

value: Wild Type

value: Dermis

value: CD64hi Dermal Macrophage

value: Uninfected Contol


title: Primed OSKLH iPSC_1 (bulkRNA-seq)


title: C2C12 cells, ShPkm2, 48 h diff, rep2


title: Primed OSKL iPSC_7 (bulkRNA-seq)


title: Primed OSKL iPSC_8 (bulkRNA-seq)


title: TR133_347_IRP2_+/+_ZT12_Rep2_totalRNA

value: liver


title: TR133_340_IRP2_+/+_ZT12_Rep2_totalRNA


title: TR132_340_IRP2_ko/ko_ZT12_Rep2_totalRNA

value: IRP2 knockout


title: C2C12 cells, ShPkm1, 48 h diff, rep1

value: Pkm1 Knockdown


title: Sc BY4741 WT, Oac, biol rep 1

value: Euroscarf #Y00000

value: MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0

value: Wild type

value: Reference strain for biol rep 1


title: Sample 32_DIPGXIII, ChIP-seq H3.3K27M, SB939

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

data_processing:
RNAseq: The sequenced paired-end reads were mapped to hg38 genome using tophat2 aligner v2.1.1 with the default parameters. The expression estimates for each gene were obtained using Bioconductor package DESeq2. TPM (Transcripts per Kilobase Million) values were calculated
ChIPseq: The paired-end fragments were generated. Reads were mapped to the to hg38 genome using Bowtie aligner version 0.12.9. Only uniquely mapped reads were retained. The reads with insert sizes <50 bp or >500 bp were removed from further analysis. Genomic positions with the numbers of mapped tags above the significance threshold of Z-score of 7 were identified as anomalous, and the tags mapped to such positions were discarded. H2A.Z, H3.3 and H3.3K27M occupancies were estimated as tag frequencies
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each RNA-seq sample
Supplementary files format and content: ChIPseq: wig files with coverage

source_name: brain

extract_protocol:
RNA-seq: RNA was isolated using RNeasy Plus Kit (Qiagen) according to manufacturer’s instructions and the quality was assessed with the Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies).
RNA-seq: PolyA-enriched RNA libraries were prepared with the KAPA Stranded mRNA Sample Preparation Kit (Kapa Biosystems).
ChIP-seq: ChIP-seq (including crosslinikng, cell lysis, chromatin digestion with Mnase, and chromatin immunoprecipitatation with H3.3 and H3.3K27M antibodies) was performed based on protocol by Cook et al.., 2017 (doi: 10.1002/cpmb.45). Eluted and input DNA was purified with phenol-chloroform extraction followed by additional purification with ZymoResearch DNA Clean & Concentrator-5 columns. Digested DNA profiles were confirmed using the 2100 Bioanalyzer with the Agilent DNA High Sensitivity chip (Agilent Technologies).
ChIP-seq: The Input and ChIP libraries were prepared using the Qiaseq Ultra Low Input Library Kit (Qiagen), according to manufacturer’s instructions.

value: brain

value: DIPGXIII

tag: antibody

value: H3.3K27M mutant


title: Sample 31_DIPGXIII, ChIP-seq H3.3K27M, DMSO

value: DMSO


title: Primed OSKL iPSC_5 (bulkRNA-seq)

value: Primed induced pluripotent stem cells

value: Female


title: TR134_340_IRP2_ko/ko_ZT12_Rep3_totalRNA


title: C2C12 cells, shScr, 48 h diff, rep 2

value: Immortalized cell line

value: Myoblasts

value: WT

value: Myoblasts differentiation (48 h)


title: Primed OSKL iPSC_4 (bulkRNA-seq)


title: Sample 30_DIPGXIII, ChIP-seq H3.3K27M, SB939


title: TR124_347_IRP1_ko/ko_ZT5_Rep3_totalRNA

value: liver

value: IRP1 Knockout


title: TR125_340_IRP1_+/+_ZT5_Rep3_totalRNA


title: TR130_340_IRP2_ko/ko_ZT12_Rep1_totalRNA

value: IRP2 knockout


title: Sample 28_SF7761, ChIP-seq H3.3K27M, SB939


title: DiFMOC-G

city: Shanghai

first: Qihang

last: Zhao

address: 800 xiangyin road

institute: National laboratory of medical immunology

description: RNA-Seq of totol cell fraction of WT mouseperitoneal macrophages treat with Sev.

data_processing:
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS)
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mouse peritoneal macrophages

extract_protocol:
RNA was harvested using TriZOL. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared according ro BGI company's standard protocols.

value: mouse peritoneal macrophages

value: macrophages

value: C57 B6/L WT

value: VSV for 12h and pre-treated with 0.4uM DiGMOC-G for 12h


title: Primed OSKL iPSC_6 (bulkRNA-seq)


title: Primed OSKL iPSC_3 (bulkRNA-seq)


title: C2C12 cells, ShPkm1, 48 h diff, rep2

value: Pkm1 Knockdown


title: TR131_340_IRP2_+/+_ZT12_Rep1_totalRNA


title: C2C12 cells, shScr, 48 h diff, rep 1


title: Sample 27_SF7761, ChIP-seq H3.3K27M, DMSO

value: brain


title: TR124_340_IRP1_ko/ko_ZT5_Rep3_totalRNA


title: Primed OSKL iPSC_1 (bulkRNA-seq)


title: Primed OSKL iPSC_2 (bulkRNA-seq)


title: T-cells allo-HSCT, d+105 ex vivo, 8-OHdG low, 5 [KMT94d105]

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

description: samples ex vivo allo-HSCT patients - no treatment ex vivo

data_processing:
Adapters were clipped by trim_galore
Sequence reads were mapped by STAR aligner
Counting with featureCounts
Analysed using edgeR, normallized with TMM method
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-delimited normalized cpm

source_name: peripheral blood

extract_protocol:
RNA was extracted using  the innuPREP DNA/RNA Mini Kit (Analytik Jena AG, Jena, Germany); on column DNAse digestion was used to remove genomic DNA contamination (RNAse-Free DNase Set, Qiagen, Venlo, Netherlands). RNA was diluted in RNase free H2O to a maximum concentration of 200 ng/μl.
INVIEW transcriptome Explore (Eurofins)

tag: condition

value: low oxidative DNA damage

value: peripheral blood

value: primary T-cells

value: Allogeneic hematopoietic stem cell transplantation (allo-HSCT)


title: DMSO

description: RNA-Seq of totol cell fraction of WT mouseperitoneal macrophages.

value: VSV for 12h


title: Sample 24_DIPGXIII, ChIP-seq H3.3, SB939

value: DIPGXIII

value: H3.3K27M mutant


title: TR123_347_IRP1_+/+_ZT5_Rep2_totalRNA

value: WT


title: R_DK_2 [N12_2]

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
GWBS (bisulfite seq) -- The reads were aligned to reference mice genome GRCm38 , following to extract genome-wide 5mC in context of CG, CHG and CHH using Bismark tool. methylKit was used to quantify levels of methylated bases and to identify differently methylated cytosines, regions and promoters (DMC, DMR and DMP). The methylation profile and DMRs in gene feature regionsTSS, TES and gene body were analysed by a Python package HMST-Seq-Analyzer pipeline.
RNA-seq --  The clean reads were aligned to reference mouse genome mm10/GRCm38 by HISAT. The transcripts from all samples were futher assembled and merged using stingTie. The DESeq2 tool was used to normalize counts and identify the differentially expressed genes.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: 5mC percentage in CG context
Supplementary_files_format_and_content: transcript count table in FPKM
Supplementary_files_format_and_content: normalized count by DESeq2

source_name: hippocampus

extract_protocol: GWBS: total DNA was extracted from hippocampus of male mice using a AllPrep DNA/RNA/Protein mini-Kit, following by bisulfite treatment and library preparision. RNA-seq: RNA extracted by AllPrep DNA/RNA/Protein mini-Kit.

tag: strain background

value: hippocampus

value: post natal 6 months

tag: genotype/variation

value: Neil1-/- Neil2 -/-


title: Sample 23_DIPGXIII, ChIP-seq H3.3, DMSO

value: DMSO


title: R_DK_1 [N12_1]

value: Neil1-/- Neil2-/-


title: TR123_340_IRP1_+/+_ZT5_Rep2_totalRNA

value: liver


title: T-cells allo-HSCT, d+100 ex vivo, 8-OHdG high, 5 [KMT89d100]

value: high oxidative DNA damage


title: Sample 22_DIPGXIII, ChIP-seq H3.3, SB939


title: Sample 29_DIPGXIII, ChIP-seq H3.3K27M, DMSO


title: TR122_347_IRP1_+/+_ZT5_Rep1_totalRNA


title: T-cells allo-HSCT, d+106 ex vivo, 8-OHdG high, 4 [KMT87d106]


title: R_Neil2_2 [N2_2]


title: T-cells allo-HSCT, d+105  ex vivo, 8-OHdG low, 4 [KMT82d105]


title: TR122_340_IRP1_+/+_ZT5_Rep1_totalRNA


title: TR121_347_IRP1_ko/ko_ZT5_Rep2_totalRNA

value: IRP1 Knockout


title: Sample 21_DIPGXIII, ChIP-seq H3.3, DMSO

value: brain


title: Sample 20_SF7761, ChIP-seq H3.3, SB939


title: T-cells allo-HSCT, d+106 ex vivo, 8-OHdG high, 3 [KMT78d106]


title: Sample 19_SF7761, ChIP-seq H3.3, DMSO


title: R_Neil1_1 [N1_1]


title: R_Neil2_1 [N2_1]


title: R_Neil1_2 [N1_2]


title: TR120_347_IRP1_ko/ko_ZT5_Rep1_totalRNA


title: TR121_340_IRP1_ko/ko_ZT5_Rep2_totalRNA


title: Sample 16_DIPGXIII, ChIP-seq H2A.Z, SB939


title: R_WT_2 [WT_2]

value: wild type


title: TR120_340_IRP1_ko/ko_ZT5_Rep1_totalRNA


title: R_WT_1 [WT_1]


title: TR112_347_IRP1_+/+_ZT12_Rep3_totalRNA


title: Sample 15_DIPGXIII, ChIP-seq H2A.Z, DMSO


title: Sample 14_DIPGXIII, ChIP-seq H2A.Z, SB939


title: T-cells allo-HSCT,d+52 ex vivo, 8-OHdG high, 1 [KMT126d52]

value: peripheral blood


title: Sample 13_DIPGXIII, ChIP-seq H2A.Z, DMSO


title: T-cells allo-HSCT, d+43 ex vivo, 8-OHdG low, 1 [KMT120d43]

value: low oxidative DNA damage

value: primary T-cells


title: G_DK_1


title: TR112_340_IRP1_+/+_ZT12_Rep3_totalRNA


title: Sample 12_SF7761, ChIP-seq H2A.Z, SB939


title: TR111_347_IRP1_ko/ko_ZT12_Rep3_totalRNA


title: T-cells of healthy donors, 72h stimulation + H2O2 treatment, donor 5 [H2O2.K392]

description: read length: 2 x 150 bp

growth_protocol: purified human T-cells were cultured in RPMI 1640 (Thermo Fischer, Waltham, MA, USA) supplemented with GlutaMAX, P/S and 10% FCS

extract_protocol:
RNA was extracted using  the innuPREP DNA/RNA Mini Kit (Analytik Jena AG, Jena, Germany); on column DNAse digestion was used to remove genomic DNA contamination (RNAse-Free DNase Set, Qiagen, Venlo, Netherlands). RNA was diluted in RNase free H2O to a maximum concentration of 200 ng/μl.
RNAseq was performed by Eurofins/GATC Biotech (INVIEW NGS transcriptome explore). Library preparation: Strand specific cDNA library; Purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis (strand specific), adapter ligation and adapter specific PCR amplification.

treatment_protocol: T-cells were incubated for 72 h with activating anti-CD2/CD3/CD28 microbeads in a 1:2 bead-to-cell ratio (Miltenyi Biotec). 10 µM H2O2 (Sigma-Aldrich, St. Louis, MO, USA) was added twice per day.

tag: disease state

value: healthy donor


title: TR111_340_IRP1_ko/ko_ZT12_Rep3_totalRNA


title: G_Neil2_2


title: Sample 11_SF7761, ChIP-seq H2A.Z, DMSO


title: T-cells of healthy donors, control, 72h stimulation, donor 5 [Ctrl.K392]

description: read length: 2 x 150 bp

value: untreated


title: G_Neil2_1


title: TR110_347_IRP1_+/+_ZT12_Rep2_totalRNA


title: Sample 8_DIPGXIII, RNA-seq, SB939

value: DIPGXIII

value: H3.3K27M mutant


title: T-cells allo-HSCT, d+105 ex vivo, 8-OHdG low, 2 [KMT51d105]

value: Allogeneic hematopoietic stem cell transplantation (allo-HSCT)


title: Sample 7_DIPGXIII, RNA-seq, DMSO


title: TR110_340_IRP1_+/+_ZT12_Rep2_totalRNA

value: WT


title: T-cells of healthy donors, control, 72h stimulation, donor 4 [Ctrl.K384]

description: read length: 2 x 150 bp


title: G_DK_2

value: hippocampus

value: post natal 6 months

value: Neil1-/- Neil2 -/-


title: G_Neil1_1


title: Sample 6_DIPGXIII, RNA-seq, SB939


title: T-cells of healthy donors, 72h stimulation + H2O2 treatment, donor 3 [H2O2.K379]

description: read length: 2 x 150 bp


title: TR109_347_IRP1_ko/ko_ZT12_Rep2_totalRNA

value: liver


title: Sample 5_DIPGXIII, RNA-seq, DMSO

value: DMSO


title: G_WT_1


title: TR108_347_IRP1_+/+_ZT12_Rep1_totalRNA


title: Sample 4_SF7761, RNA-seq,  SB939


title: T-cells of healthy donors, control, 72h stimulation, donor 3 [Ctrl.K379]

description: read length: 2 x 150 bp


title: T-cells of healthy donors, 72h stimulation + H2O2 treatment, donor 2 [H2O2.K375]

description: read length: 2 x 150 bp


title: G_Neil1_2


title: Sample 3_SF7761, RNA-seq, DMSO


title: T-cells of healthy donors, control, 72h stimulation, donor 2 [Ctrl.K375]

description: read length: 2 x 150 bp


title: TR107_340_IRP1_ko/ko_ZT12_Rep1_totalRNA

value: IRP1 Knockout